Related papers: Cooperative Function with Thermal Fluctuations in …
In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very…
The presence of attractive interaction between fermions can lead to pairing and superfluidity in an optical lattice. The temperature needed to observe superfluidity is about a tenth of the tunneling energy in the optical lattice, and…
We consider cooperative reactions and we study the effects of the interaction strength among the system components on the reaction rate, hence realizing a connection between microscopic and macroscopic observables. Our approach is based on…
We propose a new strategy to improve the self-assembly properties of DNA-functionalised colloids. The problem that we address is that DNA-functionalised colloids typically crystallize in a narrow temperature window, if at all. The…
A paradigm for isothermal, mechanical rectification of stochastic fluctuations is introduced in this paper. The central idea is to transform energy injected by random perturbations into rigid-body rotational kinetic energy. The prototype…
Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We…
In my PhD thesis I studied cooperative phenomena arise in complex systems using the methods of statistical and computational physics. The aim of my work was also to study the critical behaviour of interacting many-body systems during their…
We present a statistical mechanics treatment of the stability of globular proteins which takes explicitly into account the coupling between the protein and water degrees of freedom. This allows us to describe both the cold and the warm…
Fibrous networks are ideal functional materials since they provide mechanical rigidity at low weight. Such structures are omnipresent in natural biomaterials from cells to tissues, as well as in man-made materials from polymeric composites…
Traditionally, it is understood that fluctuations in the equilibrium distribution are not evident in thermodynamic systems of large $N$ (the number of particles in the system) \cite{Huang1}. In this paper we examine the validity of this…
We show the existence of fragile-to-strong transitions in kinetically constrained systems by studying the equilibrium and out-of-equilibrium dynamics of a generic constrained Ising spin chain which interpolates between the symmetric and…
We study the equilibrium statistical properties of the potential energy landscape of several glass models in a temperature regime so far inaccessible to computer simulations. We show that unstable modes of the stationary points undergo a…
Accurately predicting protein melting temperature changes (Delta Tm) is fundamental for assessing protein stability and guiding protein engineering. Leveraging multi-modal protein representations has shown great promise in capturing the…
Recent studies have shown that functional brain brainwork is dynamic even during rest. A common approach to modeling the brain network in whole brain resting-state fMRI is to compute the correlation between anatomical regions via sliding…
A fluctuation theorem is examined for the first-passage time of a biomolecular machine (e.g., a motor protein or an enzyme) in a nonequilibrium steady-state. For such machines in which the driven, observable process is coupled to a hidden…
Athermal models of disordered fibrous networks are highly useful for studying the mechanics of elastic networks composed of stiff biopolymers. The underlying network architecture is a key aspect that can affect the elastic properties of…
We introduce and analyze a class of heat engines composed of interacting units, in which the thermal reservoir is associated with the neighborhood surrounding each unit. These systems can be mapped onto stochastic opinion models and are…
One of the major challenges in stochastic thermodynamics is to compute the distributions of stochastic observables for small-scale systems for which fluctuations play a significant role. Hitherto much theoretical and experimental research…
We study the elastic properties of thermal networks of Hookean springs. In the purely mechanical limit, such systems are known to have vanishing rigidity when their connectivity falls below a critical, isostatic value. In this work we show…
As an example of topic where biology and physics meet, we present the issue of protein folding and stability, and the development of thermodynamics-based bioinformatics tools that predict the stability and thermal resistance of proteins and…